Ap Biology Exam Key Terms

Dehydration synthesis

process by which monomers are bonded together to form a polymer with the release of water. A water molecule is removed (H from one molecule, OH from another)

Oxidation / Reduction

Oxidation = the loss of electrons, loss of hydrogen, or gain of oxygen by a substance.

Reduction = the gain of electrons, gain of hydrogen, or loss of oxygen by a substance.

Adhesion / Cohesion

Cohesion = the attraction between molecules of the same substance.

Cohesion = the attraction between molecules of the same substance.

Disaccharide

carbohydrate made of two monosaccharide units joined together by a glycosidic bond.

Steroid

type of lipid characterized by a four-ring carbon structure. Form hormones that regulate body processes.

Eg. Testosterone and estrogen

Amino acid

organic molecule with an amino group (–NH₂) and a carboxyl group (–COOH) that links with others to form proteins. The basic building block of proteins.

Allosteric regulation

control of an enzyme’s activity by the binding of a molecule at a site other than the active site, called the allosteric site.

• This causes a change in enzyme shape

• The change increases or decreases enzyme activity

Fluid mosaic mode

describes the cell membrane as a fluid phospholipid bilayer with embedded proteins forming a mosaic pattern.

Hypertonic/Hypotonic/Isotonic

hypertonic = has a higher solute concentration than the cell

hypotonic = has a lower solute concentration than the cell.

isotonic = has the same solute concentration as the cell.

Activation energy

minimum amount of energy required to start a chemical reaction.

Endergonic reaction

a reaction that absorbs energy because the products have more free energy than the reactants.

eg.Photosynthesis: 6CO2 + 6H2O + light energy→ C6H12O6 + 6O2 ~ endothermic rxn

Aerobic respiration

oxygen-requiring process that breaks down glucose to produce ATP (energy) , carbon dioxide, and water.

Glycolysis

first step of cellular respiration, in which one glucose molecule (6C) is broken down into two molecules of pyruvate (3C), producing a net gain of 2 ATP and 2 NADH.

Chemiosmosis

The movement of protons across a membrane through ATP synthase, using the proton gradient to produce ATP.

Antenna complex

a cluster of pigments in the thylakoid membrane that captures light energy and transfers it to the photosystem reaction center.

Light independent reaction / Calvin cycle

phase of photosynthesis that uses ATP and NADPH from the light-dependent reactions to fix carbon dioxide into glucose.

*does not require light directly

Stroma

the fluid-filled space inside the chloroplast surrounding the thylakoids, where the light-independent reactions (Calvin cycle) take place.

NADP/NADPH

NADP⁺ is an electron carrier that accepts electrons to form NADPH, which provides reducing power for the Calvin cycle.

NADP⁺ (Nicotinamide Adenine Dinucleotide Phosphate) – oxidized form, which can accept electrons and hydrogen ions.

NADPH – reduced form, which carries high-energy electrons for biosynthetic reactions.

Hydrolysis

chemical reaction where a water molecule is used to break a bond in a larger molecule, resulting in smaller molecules.

Hydrogen bond

a weak attractive force that forms between a hydrogen atom covalently (non-metals) bonded to a highly electronegative atom (like O, N, or F) and another electronegative atom

Functional group

specific group of atoms within a molecule that determines the chemical properties and reactions of that molecule.

Polysaccharide

carbohydrate made of many monosaccharide units linked together by glycosidic bonds.

Fatty acid

a long chain of hydrocarbon with a carboxyl group (–COOH) at one end. It is a basic building block of fats (triglycerides) and phospholipids.

Denaturation

Competitive inhibitor

the structural change of a protein that results in the loss of its structure and function due to heat, pH, or chemicals.

Integral membrane protein

a protein that is embedded within the phospholipid bilayer of a cell membrane and often spans across the membrane.

Functions:

1. Transport – channels or carriers for ions and molecules

2. Signal transduction – receptors for hormones and neurotransmitters

3. Cell recognition – glycoproteins for immune response

4. Anchoring – attach cytoskeleton to the membrane

Active transport

movement of molecules across a cell membrane from a region of lower concentration to a region of higher concentration, using energy (usually from ATP).

*going against their concentration gradient

Kinetic vs Potential energy

Kinetic = Energy of motion; energy an object or particle has because it is moving.

potential = Stored energy due to the position or structure of an object or system.

Exergonic reaction

chemical reaction that releases energy because the products have less free energy than the reactants.

Eg. Cellular respiration – breakdown of glucose → CO₂ + H₂O + energy ~ exothermic

Anaerobic respiration

breakdown of glucose (or other organic molecules) without oxygen to release energy (ATP) and produce smaller molecules eg. lactic acid

Pyruvate oxidation

(also called the link reaction) = process where pyruvate from glycolysis is converted into Acetyl-CoA, producing NADH and CO₂ in preparation for the Krebs cycle.

Polar covalent bond

type of covalent bond in which electrons are shared unequally between two atoms, resulting in a partial positive charge (δ⁺) on one atom and a partial negative charge (δ⁻) on the other.

Eg. Water (H₂O) – Oxygen is δ⁻, Hydrogens are δ⁺ → hydrogen bonds form

Reaction centre

Primary electron acceptor

specialized chlorophyll molecule in a photosystem that receives energy from the antenna complex and uses it to excite electrons, initiating the light-dependent reactions of photosynthesis.

*Found in Photosystem I (PSI) and Photosystem II (PSII)

Stomata

small openings/pores on the surface of leaves and stems that allow for gas exchange and water loss between the plant and the environment.

C4 plants

plants that fix CO2 into a 4-carbon compound (oxaloacetate) before entering the Calvin cycle, allowing them to efficiently photosynthesize under high light, high temperature, and low CO₂ (hot/dry) conditions.

Hydrophilic

molecules or parts of molecules that interact/dissolve well with water because they are polar or charged.

Ether/Ester/Peptide linkages

ether linkage = a bond formed between two carbon atoms via an oxygen atom (C–O–C).

ester linkage = a bond formed between a carboxyl group (–COOH) of a fatty acid and the hydroxyl group (–OH) of glycerol (–COOH + –OH)

peptide linkage = a bond formed between the amino group (–NH₂) of one amino acid and the carboxyl group (–COOH) of another, releasing water (–COOH + –NH₂)

Triglyceride

a lipid composed of one glycerol molecule and three fatty acids joined by ester bonds, used for energy storage.

Protein

a large, complex macromolecule made of one or more chains of amino acids linked by peptide bonds, performing structural, enzymatic, transport, and regulatory functions.

Induced fit mode

describes how an enzyme changes its shape slightly when a substrate binds, so the enzyme fits more snugly around the substrate, enhancing the reaction.

Peripheral membrane protein

a protein that loosely attaches temporarily to the surface of the cell membrane, functioning in signaling, enzymatic activity, or structural support.

• – act as receptors or part of signaling pathways

• – catalyze reactions near the membrane

• – attach to carbohydrates on glycoproteins

Facilitated diffusion

passive movement of molecules across a cell membrane through specific transport proteins, down their concentration gradient, without using energy.

Free energy

the portion of a system’s total energy that can be used to do work at constant temperature and pressure. determining whether a reaction is spontaneous or not.

Entropy

the measure of disorder/randomness in a system, with natural processes tending to increase total entropy.

Substrate level phosphorylation

the direct transfer of a phosphate group from a high-energy substrate molecule to ADP, forming ATP without the involvement of an electron transport chain.

Kreb’s / Citric acid cycle

a series of enzyme-catalyzed reactions in the mitochondrial matrix that oxidize Acetyl-CoA to produce CO₂, high-energy electron carriers (NADH, FADH₂), and ATP

FAD / FADH2

FAD is an electron carrier that is reduced to FADH₂ in the Krebs cycle and donates electrons to the ETC to produce ATP.

• FAD (Flavin Adenine Dinucleotide) – an oxidized coenzyme that can accept electrons.

• FADH₂ – the reduced form of FAD after it gains electrons and hydrogen ions.

Photosystem

a protein-pigment complex in the thylakoid membrane that captures light energy and converts it into chemical energy during the light-dependent reactions of photosynthesis.

PSII → ETC → PSI → NADPH

Two main types: Photosystem I (PSI) and Photosystem II (PSII)

PSII – absorbs light at 680 nm, generates high-energy electrons, splits water

PSI – absorbs light at 700 nm, excites electrons → NADP⁺ reduced to NADPH

Grana

stacks of thylakoid membranes in the chloroplast where the light-dependent reactions of photosynthesis take place.

Guard cells

specialized kidney-shaped cells surrounding stomata that regulate the opening and closing of the stomatal pore, controlling gas exchange and water loss in plants.

CAM (Crassulacean Acid Metabolism) plants

plants that open their stomata at night to fix CO₂ into organic acids and close them during the day, allowing photosynthesis to occur while minimizing water loss in arid conditions.

Eg. pineapple, cactus

Redox reaction

chemical reaction in which electrons are transferred between molecules, involving oxidation (loss of electrons) and reduction (gain of electrons).

Eg. cellular respiration

• Glucose is oxidized → CO₂

• Oxygen is reduced → H₂O

Hydrophobic

molecules or parts of molecules that repel water or do not interact well with water, usually because they are non-polar. often found in fats

Monosaccharide

the simplest form of carbohydrate(suagr unit) , consisting of a single sugar unit thatserves as an energy source and building block for larger carbohydrates

Eg. Gucose

Isomer

molecules that have the same molecular formula but different structural arrangements and therefore different properties.

Eg. Glucose vs. fructose

4 levels of protein formation

Proteins have four levels of structural organization, which determine their shape and function.

1. Primary structure = The linear sequence of amino acids in a polypeptide chain.

2. secondary structure = The local folding of the polypeptide chain into α-helix or β-pleated sheet due to hydrogen bonds.

3. Tertiary structure = 3D folding of the entire polypeptide chain due to interactions among R-groups (side chains)

4. Quaternary structure = assembly of two or more polypeptide chains into a single functional protein.

Substrate

the specific reactant molecule that binds to an enzyme’s active site and undergoes a chemical reaction to form a product.

Enzyme + Substrate → Product

Non-competitive inhibition

when an inhibitor binds to an enzyme at a site other than the active site, changing its shape and reducing activity regardless of substrate concentration.

Passive transport

movement of molecules across a cell membrane without the use of energy (ATP), down their concentration gradient.

Metabolism

the sum of all chemical reactions that occur in a living organism to maintain life, including breaking down molecules to release energy and building new molecules for growth and repair.

Laws of thermodynamics

how energy is transferred and transformed in biological systems.

state that energy is conserved (1st law), entropy increases in energy transfers (2nd law), and entropy approaches zero at absolute zero (3rd law).

1st. Energy cannot be created or destroyed, only converted from one form to another.

2nd. In any energy transfer, some energy is lost as heat, increasing the entropy (disorder) of the universe.

3nd. As temperature approaches absolute zero (0 K), the entropy of a perfect crystal approaches zero.

Phosphorylation

the addition of a phosphate group (PO₄³⁻) to a molecule, often regulating its activity or storing/transferring energy.

important for energy transfer, enzyme regulation, and signaling.

Oxidative phosphorylation

ATP production using electrons from NADH/FADH₂, oxygen, and a proton gradient across the inner mitochondrial membrane.

• Location: Inner mitochondrial membrane

• Requires oxygen → aerobic process

• Process:

  1. Electrons pass through ETC protein complexes → energy released

  2. Energy pumps H⁺ ions into the intermembrane space → creates a proton gradient

  3. H⁺ ions flow back through ATP synthase → drives ATP production

• Produces ~28–34 ATP per glucose, the majority of cellular ATP

Electron transport chain

(ETC) is a series of protein complexes and electron carriers in the inner mitochondrial membrane that transfer electrons from NADH and FADH₂ to oxygen, releasing energy to pump protons and create a proton gradient for ATP synthesis.

Decarboxylation

the removal of a carboxyl group (–COOH) from a molecule, releasing carbon dioxide (CO₂).

Eg. Pyruvate → Acetyl-CoA + CO₂ (catalyzed by pyruvate dehydrogenase)

Light dependent reaction

the stage of photosynthesis that requires light to produce ATP, NADPH, and oxygen by capturing energy from sunlight in the thylakoid membranes of chloroplasts.

• Location: Thylakoid membranes

• Requires: Light and water (H₂O)

Thylakoid

a membrane-bound sac inside a chloroplast where the light-dependent reactions of photosynthesis occur.

ocation: Inside the chloroplast, stacked into grana

Rubisco

(Ribulose-1,5-bisphosphate carboxylase/oxygenase) is the enzyme that catalyzes the fixation of carbon dioxide (CO₂) to ribulose-1,5-bisphosphate (RuBP) during the Calvin cycle in photosynthesis.

• Location: Stroma of chloroplasts

• Function: Catalyzes the first major step of carbon fixation in the Calvin cycle

• Abundance: Most abundant enzyme on Earth

Chlorophyll

a green pigment found in the chloroplasts of plants, algae, and cyanobacteria that absorbs light energy for photosynthesis.

• Chlorophyll a – primary pigment, directly participates in the light reactions

• Chlorophyll b – accessory pigment, broadens the spectrum of light absorbed

Purine

nitrogenous bases with a double-ring structure, including adenine and guanine, that pair with pyrimidines in nucleic acids.

Conservative replication

a model in which the original DNA stays intact and a completely new DNA molecule is synthesized from free nucleotides but it does not occur in real cells.

DNA gyrase

an enzyme that relieves supercoiling and tension in the DNA double helix ahead of the replication fork during DNA replication.

Replication bubble

a region of DNA where the double helix has unwound and separated into two single strands, allowing DNA replication to occur at the same time in both directions.

DNA polymerase III

the main enzyme that synthesizes new DNA strands by adding nucleotides to a primer and proofreading for errors.

• Direction of synthesis: 5′ → 3′

• Requires: A RNA primer to start synthesis (made by primase)

Telomere

repetitive DNA sequences at chromosome ends that protect them from damage, shortening, and deterioration during replication.

Messenger RNA

(mRNA) is a type of RNA that carries the genetic information from DNA in the nucleus to the ribosomes in the cytoplasm, where it serves as a template for protein synthesis.

Template strand

the DNA strand that serves as a guide for RNA synthesis during transcription, allowing complementary RNA nucleotides to be assembled.

Orientation: 3′ → 5′ (RNA is synthesized 5′ → 3′)

TATA box

DNA sequence (consensus: TATAAA) found in the promoter region of eukaryotic genes that helps position RNA polymerase for transcription to start at the correct site.

Anticodon

a three-nucleotide sequence on tRNA that pairs with an mRNA codon to ensure correct amino acid incorporation.

Substitution

a type of gene mutation in which one nucleotide in the DNA sequence is replaced by another, potentially changing the amino acid sequence of the protein.

Nonsense mutation

is a nucleotide change that converts a codon into a stop codon, resulting in premature termination of protein synthesis.

Restriction enzyme

(restriction endonuclease) is an enzyme that cuts DNA at specific DNA sequences, producing fragments that can be used in genetic analysis and molecular cloning.

Pyrimidine

single-ring nitrogenous bases, including cytosine, thymine, and uracil, that pair with purines in nucleic acids.

• Cytosine (C) → Guanine (G)

• Thymine (T) → Adenine (A)

Semiconservative replication

process where each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.

Replication fork

the Y-shaped region at the site of DNA replication where the double-stranded DNA is unwound into two single strands, allowing new DNA synthesis to occur.

RNA primase

an enzyme that synthesizes short RNA primers on a DNA template to allow DNA polymerase to start replication.

Leading strand

the DNA strand that is synthesized continuously in the same direction as the replication fork movement during DNA replication.

Direction of synthesis: 5′ → 3′ (toward the replication fork)

Central dogma

states that genetic information flows from DNA → RNA → Protein

• DNA replication: DNA → DNA (copies genetic material)

• Transcription: DNA → RNA (mRNA carries the code)

• Translation: mRNA → Protein (amino acid sequence forms a polypeptide)

• Direction: Information does not flow from protein back to nucleic acids

Transfer RNA

(tRNA) is a type of RNA that carries amino acids to the ribosome and pairs its anticodon with mRNA codons during translation.

Codon

a three-nucleotide sequence on mRNA that specifies an amino acid or a stop signal during protein synthesis.

• Start codon: AUG → signals the beginning of translation and codes for Methionine

• Stop codons: UAA, UAG, UGA → signal termination of translation

Poly-A tail

a string of adenine nucleotides added to the 3′ end of mRNA that protects it from enzymatic degradation and aids in translation.

Length: Usually 50–250 adenine nucleotides

Operator

a segment of DNA in an operon that acts as a binding site for a repressor protein, controlling whether the genes of the operon are transcribed.

Insertion

a type of gene mutation in which one or more nucleotides are added into a DNA sequence, potentially altering the reading frame of a gene.

Eg.

• Original sequence: THE CAT ATE

• After insertion of “X”: THE XCA TAT E → changes codons downstream

Frameshift mutation

an insertion or deletion that shifts the reading frame of a gene, altering all downstream amino acids.

Eg.

• Original mRNA codons: THE CAT ATE THE RAT

• After deletion of “C”: THE ATA TET HER AT… → all downstream codons changed

Blunt end / Sticky end

Blunt ends are straight-cut DNA fragments, while sticky ends are staggered with overhangs that can pair with complementary sequences.

• Blunt end = types of DNA fragment ends produced by restriction enzymes when they cut DNA.

• Sticky end = DNA is cut staggered, leaving short single-stranded overhangs at each end.

Nucleotide

tthe basic unit (monomer) of DNA and RNA, consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

Eg.

Nitrogenous base

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T – DNA), Uracil (U – RNA)

DNA helicase

enzyme that unwinds and separates the two strands of the DNA double helix by breaking the hydrogen bonds between complementary bases during DNA replication.

Topoisomerase

enzyme that prevents DNA supercoiling by cutting, untwisting, and rejoining DNA strands during replication.

RNA primer

a short RNA sequence that provides a starting point for DNA polymerase during DNA replication.

• Leading strand: one primer needed

• Lagging strand: many primers needed (one for each Okazaki fragment)